An quick survey of human 2-point linkage analysis Terry Speed Division of Genetics & Bioinformatics, WEHI Department of Statistics, UCB NWO/IOP Genomics Winterschool Mathematics and Biology December 17, 2001 Lecture 2

Modern genetics began with Mendel’s experiments on garden peas. He studied seven contrasting pairs of characters, including: The form of ripe seeds: round, wrinkled The color of the seed albumen: yellow, green The length of the stem: long, short Mendel’s first law: Characters are controlled by pairs of genes which separate during the formation of the reproductive cells (meiosis) A a A a Mendel’s two laws

Mendel’s second law When two or more pairs of genes segregate simultaneously, they do so independently. A a; B b A BA bA ba Ba ba b

“Exceptions” to Mendel’s Second Law Morgan’s fruitfly data (1909): 2,839 flies Eye colorA: reda: purple Wing lengthB: normalb: vestigial AABB x aabb AaBb x aabb AaBb Aabb aaBb aabb Exp Obs 1, ,195

Morgan’s explanation A A BB a a b b  F1: A a Bb a a b b  F2: A a Bb a a b b A a bb a a B b Crossover has taken place

Parental types:AaBb, aabb Recombinants: Aabb, aaBb The proportion of recombinants between the two genes (or characters) is called the recombination fraction between these two genes. It is usually denoted by r or . For Morgan’s traits: r = ( )/2839 = If r < 1/2: two genes are said to be linked. If r = 1/2: independent segregation (Mendel’s second law). Now we move on to (small) pedigrees.

One locus: founder probabilities Founders are individuals whose parents are not in the pedigree. They may of may not be typed. Either way, we need to assign probabilities to their actual or possible genotypes. This is usually done by assuming Hardy-Weinberg equilibrium. (There is a good story here.) If the frequency of D is.01, H-W says pr(Dd ) = 2x.01x.99 Genotypes of founder couples are (usually) treated as independent. pr(pop Dd, mom dd ) = (2x.01x.99)x(.99) 2 D d dd 1 21

One locus: transmission probabilities Children get their genes from their parents’ genes, independently, according to Mendel’s laws; also independently for different children. D d d 3 21 pr(kid 3 dd | pop 1 Dd & mom 2 Dd ) = 1/2 x 1/2

One locus: transmission probabilities - II D d pr(3 dd & 4 Dd & 5 DD | 1 Dd & 2 Dd ) = (1/2 x 1/2)x(2 x 1/2 x 1/2) x (1/2 x 1/2). The factor 2 comes from summing over the two mutually exclusive and equiprobable ways 4 can get a D and a d. d D

One locus: penetrance probabilities Pedigree analyses usually suppose that, given the genotype at all loci, and in some cases age and sex, the chance of having a particular phenotype depends only on genotype at one locus, and is independent of all other factors: genotypes at other loci, environment, genotypes and phenotypes of relatives, etc. Complete penetrance: pr(affected | DD ) = 1 Incomplete penetrance: pr(affected | DD ) =.8 DD

One locus: penetrance - II Age and sex-dependent penetrance (see liability classes) pr( affected | DD, male, 45 y.o. ) =.6 D D (45)

One locus: putting it all together Assume penetrances pr(affected | dd ) =.1, pr(affected | Dd ) =.3 pr(affected | DD ) =.8, and that allele D has frequency.01. The probability of this pedigree is the product: (2 x.01 x.99 x.7) x (2 x.01 x.99 x.3) x (1/2 x 1/2 x.9) x (2 x 1/2 x 1/2 x.7) x (1/2 x 1/2 x.8) D d d D In general shaded means affected, blank means unaffected.

One locus: putting it all together - II Note that we begin by multiplying founder gene frequencies, followed by founder penetrances. Next we multiply transmission probabilities, followed by penetrance probabilities of offspring, using their independence given parental genotypes. If there are missing or incomplete data, we must sum over all mutually exclusive possibilities compatible with the observed data. The general strategy of beginning with founders, then non-founders, and multiplying and summing as appropriate, has been codified in what is known as the Elston-Stewart algorithm for calculating probabilities over pedigrees. It is one of the two widely used approaches. The other is termed the Lander-Green algorithm and takes a quite different approach. Both are hidden Markov models, both have compute time/space limitations with multiple individuals/loci (see next), and extending them beyond their current limits is the ongoing outstanding problem.

Two loci: linkage and recombination Son 3 produces sperm with D-T, D-t, d-T or d-t in proportions: 3 21 D d T t d t D T 3

Two loci: linkage and recombination - II Son produces sperm with DT, Dt, dT or dt in proportions:  = 1/2 : independent assortment (cf Mendel) unlinked loci  < 1/2 : linked loci  ≈ 0: tightly linked loci Note:  > 1/2 is never observed If the loci are linked, then D-T and d-t are parental, and D-t and d-T are recombinant haplotypes

ˆ Recombination only discernible in the father. Here  = 1/4 (why?) This is called the phase-known double backcross pedigree. Two loci: estimation of recombination fractions D T d t D d t d t D d T t D d T t D d T t d t

Two loci: phase D d T t d t D d T t Suppose we have data on two linked loci as follows: Was the daughter’s D-T from her father a parental or recombinant combination? This is the problem of phase: did father get D-T from one parent and d-t from the other? If so, then the daughter's paternally derived haplotype is parental. If father got D-t from one parent and d-T from the other, these would be parental, and daughter's paternally derived haplotype would be recombinant.

Two loci: dealing with phase Phase is incompleteness in genetic information, specifically, in parental origin of alleles at heterozygous loci. Often it can be inferred with certainty from genotype data on parents. Often it can be inferred with high probability from genotype data on several children. In general genotype data on relatives helps, but does not necessarily determine phase. In practice, probabilities must be calculated under all phases compatible with the observed data, and added together. The need to do so is the main reason linkage analysis is computationally intensive, especially with multilocus analyses.

Two loci: founder probabilities Two-locus founder probabilities are typically calculated assuming linkage equilibrium, i.e. independence of genotypes across loci. If D and d have frequencies.01 and.99 at one locus, and T and t have frequencies.25 and.75 at a second, linked locus, this assumption means that DT, Dt, dT and dt have frequencies.01 x.25,.01 x.75,.99 x.25 and.99 x.75 respectively. Together with Hardy-Weinberg, this implies that pr(DdTt ) = (2 x.01 x.99) x (2 x.25 x.75) = 2 x (.01 x.25) x (.99 x.75) + 2 x (.01 x.75) x (.99 x.25). This last expression adds haplotype pair probabilities. Dd Tt

Two loci: transmission probabilities D d T t d t D d T t Initially, this must be done with haplotypes, so that account can be taken of recombination. Then terms like that below are summed over possible phases. Here only the father can exhibit recombination: mother is uninformative. pr(kid DT/dt | pop DT/dt & mom dt/dt ) = pr(kid DT | pop DT/dt ) x pr(kid dt | mom dt/dt ) = (1-  )/2 x 1.

Two Loci: Penetrance In all standard linkage programs, different parts of phenotype are conditionally independent given all genotypes, and two-loci penetrances split into products of one-locus penetrances. Assuming the penetrances for DD, Dd and dd given earlier, and that T,t are two alleles at a co-dominant marker locus. Pr( affected & Tt | DD, Tt ) = Pr(affected | DD, Tt )  Pr(Tt | DD, Tt ) = 0.8  1

Two loci: phase unknown double backcross We assume below pop is as likely to be DT / dt as Dt / dT. d t D d T t D d T t D d t d t D d T t Pr (all data |  ) = pr(parents' data |  )  pr(kids' data | parents' data,  ) = pr(parents' data)  {[((1-  )/2) 3   /2]/2+ [(  /2) 3  (1-  )/2]/2} ˆ This is then maximised in , in this case numerically. Here  = 0.5

Log (base 10) odds or LOD scores Suppose pr(data |  ) is the likelihood function of a recombination fraction  generated by some 'data', and pr(data | 1/2) is the same likelihood when  = 1/2. Statistical theory tells us that the ratio L = pr(data |  *) / pr(data | 1/2) provides a basis for deciding whether  =  * rather than  = 1/2. This can equally well be done with Log 10 L, i.e. LOD(  * ) = Log 10 {pr(data |  *) / pr(data | 1/2)} measures the relative strength of the data for  =  * rather than  = 1/2. Usually we write , not  * and calculate the function LOD(  ).

Facts about/interpretation of LOD scores Positive LOD scores suggests stronger support for  * than for 1/2, negative LOD scores the reverse. Higher LOD scores means stronger support, lower means the reverse. LODs are additive across independent pedigrees, and under certain circumstances can be calculated sequentially. For a single two-point linkage analysis, the threshold LOD  3 has become the de facto standard for "establishing linkage", i.e. rejecting the null hypothesis of no linkage. When more than one locus or model is examined, the remark in 4 must be modified, sometimes dramatically.

LOD scores for phase known double backcross families Recombination fraction

LOD scores for phase unknown double backcross families Recombination fraction

Assumptions underpinning most 2-point human linkage analyses Founder Frequencies: Hardy-Weinberg, random mating at each locus. Linkage equilibrium across loci, known allele frequencies; founders independent. Transmission: Mendelian segregation, no mutation. Penetrance: single locus, no room for dependence on relatives' phenotypes or environment. Known (including phenocopy rate). Implicit: phenotype and genotype data correct, marker order and location correct Comment: Some analyses are robust, others can be very sensitive to violations of some of these assumptions. Non-standard linkage analyses can be developed.

Acknowledgements Melanie Bahlo, WEHI Hongyu Zhao, Yale The real challenge is multipoint linkage analysis, but going there would take more time than we have today. Next in importance is dealing with two-locus penetrances, Beyond two-point human linkage analysis

References HLK Whitehouse: Towards an Understanding of the Mechanism of Heredity, 3rd ed. Arnold 1973 Kenneth Lange: Mathematical and statistical methods for genetic analysis, Springer 1997 Elizabeth A Thompson: Statistical inference from genetic data on pedigrees, CBMS, IMS, Jurg Ott : Analysis of human genetic linkage, 3rd edn Johns Hopkins University Press 1999 JD Terwilliger & J Ott : Handbook of human genetic linkage Johns Hopkins University Press 1994.